On 19 February 1894 he received his doctorate from the University of Amsterdam with a dissertation on Zechariah 9-14. He served the congregations of Rottevalle until 1895, Warga 1895-1899, Wormerveer 1899-1901, and Amsterdam from 1901 until his retirement in 1930. His sermons, like those of his father, drew large audiences even outside the Mennonite fold. He published three volumes of sermons: Als ziende den Onzienlijke (Amsterdam, 1923), In de schuilplaats des Allerhoogsten (Amsterdam, 1926), and Vernieuwd van dag tot dag (Amsterdam, 1930). He also wrote Industrie en persoonlijkheid (Haarlem, 1915), Het toevertrouwde goed (n.p., n.d.), Geschiedenis van het volk Gods in het Oude Testament (Amsterdam, 1933), Geschiedenis van het volk Gods in het Nieuwe Testament (Amsterdam, 1934), Heilig onze gedachten (Amsterdam, 1938). Numerous devotional contributions appeared in the magazine Overdenkingen, of which he was co-editor. Kuiper was active in the Gemeentedagbeweging, and promoted the cause of missions among the Dutch Mennonites. From 1914-1924 he was chairman of the Doopsgezinde Zendingsvereniging. He was also active in the peace movement and was for some time a member of the executive committee of Kerk en Vrede. Frits Kuiper, a minister in Amsterdam, was his son.